Align DUF5009 domain-containing protein (characterized, see rationale)
to candidate 5208607 Shew_1118 hypothetical protein (RefSeq)
Query= uniprot:A0KZW6 (395 letters) >FitnessBrowser__PV4:5208607 Length = 387 Score = 567 bits (1460), Expect = e-166 Identities = 273/378 (72%), Positives = 311/378 (82%), Gaps = 5/378 (1%) Query: 23 KRQSKPRLMSLDALRGFDMFWILGGEALFGALLMLTGWAGWQWGDTQMHHSEWNGFRFYD 82 K +KPRLMSLDALRGFDMFWILGGEALF ALL+ TGW GW+ D QMHHS+W+GF FYD Sbjct: 10 KPAAKPRLMSLDALRGFDMFWILGGEALFAALLVWTGWQGWRIADAQMHHSQWHGFTFYD 69 Query: 83 LIFPLFIFLSGVALGLSPKRLDKLPMQERMPVYRHGIKRLFLLLLLGILYNHGWGTGAPA 142 LIFPLFIFLSGVALGLSPKRLD LP ER+P+YRH IKRL LLLL G+LYNHGWGTG P Sbjct: 70 LIFPLFIFLSGVALGLSPKRLDSLPWPERLPLYRHAIKRLMLLLLFGVLYNHGWGTGMPM 129 Query: 143 DPEKVRYASVLGRIAFAWFFAALLVWHTSLRTQVLVALGILVAYGAVQLWLPFPGGQAGV 202 ++VRYASVLGRIAFAWFFAALLVWHT L+TQ+LVA+GIL+ Y A+QLWLP PGG AG Sbjct: 130 AADEVRYASVLGRIAFAWFFAALLVWHTDLKTQILVAIGILLGYAAMQLWLPVPGGVAGD 189 Query: 203 LSPTESINAYVDSLLLPGVSYQGRTPDPEGVLSTLPAVVNALAGVFVGHFIVKSHP---- 258 S + SINAYVD LPG+SYQGR DPEG+LSTLPA+VNALAGVF G FIVKSHP Sbjct: 190 FSISGSINAYVDGKFLPGISYQGRATDPEGILSTLPAIVNALAGVFTGRFIVKSHPKWGG 249 Query: 259 -KGEWAKVGLLSVAGGVCLALGWLLGGVIPVNKELWTSSFVLVTSGWSMLLLALFYALVD 317 KGEWAKVG+L +AG + L LGWL+ IPVNK+LWTSSFV+VT GWS++LLA+FYALVD Sbjct: 250 VKGEWAKVGILLLAGLLSLGLGWLMNPYIPVNKDLWTSSFVMVTLGWSLILLAIFYALVD 309 Query: 318 VLKWQKLAFIFVVIGTNAIIIYLASSLVDWKYIAQSVFGGVIAVLPENAQPLGAVIGLLT 377 VLK +LAF FVVIG NAIIIYLASSLV W Y+A S+FGG I LP QPL + +L Sbjct: 310 VLKLHRLAFGFVVIGCNAIIIYLASSLVKWDYLASSLFGGAIQALPIEMQPLASACAMLL 369 Query: 378 VQWLVLYWMYRRNIFVRI 395 VQWL+LYWMY+R IF+++ Sbjct: 370 VQWLLLYWMYKRGIFIKV 387 Lambda K H 0.326 0.141 0.457 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 723 Number of extensions: 34 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 395 Length of database: 387 Length adjustment: 31 Effective length of query: 364 Effective length of database: 356 Effective search space: 129584 Effective search space used: 129584 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory